I have run qdec for a simple contrast comparing thickness across the cortical surface between a patient and control group. Not much survives vertex-wise FDR correction, and I would like to try cluster-based thresholding. I would like to make sure I understand the inputs to the command. Am I correct on the following?
--thmin = the vertexwise threshold for determining clusters, where 2 corresponds to p=.01
--minarea = the cluster extent threshold - Am I correct in assuming this should not be smaller than the smoothing kernel?
When I run the command below, I get the following output. Only one (whole hemi) cluster is identified. I'm not sure if its a problem in my command line, or with my data. Also, I seem to have the --cwsig flag wrong, but can't figure out the error (appending .w or .label to the end of the output filename does not change the error).
mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh --subject fsaverage --hemi lh --surf white --annot aparc --sign abs --thmin 2 --minarea 25 --sum stats/qdec_run/cluster/summary.txt --o stats/qdec_run/cluster/cluster_output --cwsig stats/qdec_run/cluster/cwsig --olab stats/qdec_run/cluster/MF_group_lh_thk
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $
hemi = lh
srcid = qdec/MF_group_lh/contrasts.sig.mgh paint
srcsubjid = fsaverage
srcsurf = white
srcframe = 0
thsign = abs
thmin = 2
thmax = -1
fdr = -1
minarea = 25
xfmfile = talairach.xfm
nth = -1
outid = stats/qdec_run/cluster/cluster_output paint
sumfile = stats/run2/cluster/summary.txt
subjectsdir = /data/kang/work/struct/alex/freesurfer/subjects_cann
FixMNI = 1
------------- XFM matrix (RAS2RAS) ---------------
/data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/mri/transforms/talairach.xfm
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
----------------------------------------------------
Reading source surface /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/surf/lh.white
reading group avg surface area 822 cm^2 from file
Reading in average area /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/surf/lh.white.avg.area.mgh
Done reading source surface
Reading annotation /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
Computing metric properties
Loading source values
number of voxels in search space = 163842
Done loading source values (nvtxs = 163842)
overall max = 43.1907 at vertex 101931
overall min = 7.66111 at vertex 28089
surface nvertices 163842
surface area 65416.985991
surface area 65416.985976
NOT Adjusting threshold for 1-tailed test
Searching for Clusters ...
thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=25.000000
Found 1 clusters
Max cluster size 103339.460938
INFO: fixing MNI talairach coordinates
Saving thresholded output to stats/qdec_run/cluster/cluster_output
avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191
Saving cluster pval stats/qdec_run/cluster/cwsig
unknown file type for file (stats/qdec_run/cluster/cwsig)
LabelWrite: saving to stats/qdec_run/cluster/MF_group_lh_thk-0001.label
Alex Fornito
JN Peters Research Fellow
Melbourne Neuropsychiatry Centre
Department of Psychiatry
The University of Melbourne
Postal address:
Melbourne Neuropsychiatry Centre
National Neuroscience Facility
Levels 2 & 3, 161 Barry St
Carlton South Vic 3053 Australia
Ph: +61 3 8344 1861
Fax: +61 3 9348 0469